Evaluation of the STR typing kit PowerPlexk 16 with respect to technical performance and population genetics: a multicenter study

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1 International Congress Series 1239 (2003) Evaluation of the STR typing kit PowerPlexk 16 with respect to technical performance and population genetics: a multicenter study L. Henke a, *, A. Aaspollu b, R. Biondo c, B. Budowle d, K. Drobnic e, P.H. van Eede f, H. Felske-Zech g, L. Fernández de Simón h, L. Garafano i, C. Gehrig j, C. Luckenbach k, N. Malik l, M. Muche m, W. Parson n, D. Primorac o, P.M. Schneider p, J. Thomson q, D. Vanek r a Institut fuer Blutgruppenforschung, Cologne, Germany b National Institute of Chemical Physics and Biophysics, Laboratory of Molecular Genetics, Tallin 23, Estonia c Direzione Centrale della Polizia Criminale, Servizio Polizia Scientifica, Rome, Italy d FBI, Laboratory Division, Washington, DC, USA e Ministry of the Interior, 1000 Ljubljana, Slovenia f Sanquin, CLB Diagnostic Services, Immunogenetics, 1006 AD Amsterdam, Netherlands g Institut f. Rechtsmedizin, Freie Universitaet Berlin, Berlin, Germany h Instituto National de Toxicologia, Seccion de Biologia, Madrid, Spain i Raggruppamento Carabinieri Investigazoni Scientifiche, Sottocentro di Parma, Parma, Italy j Institut de Médecine Légale, 1211 Geneva 4, Switzerland k Institut für humangenetische Analytik, Tuebingen, Germany l Institut für Rechtsmedizin, Forensische Molekularbiologie, Universitaet Bern, 3012 Berne, Switzerland m Institut für Blutgruppenserologie und Genetik, Hamburg, Germany n Institut fuer Rechtsmedizin, Universitaet Innsbruck, 6020 Innsbruck, Austria o Laboratory for Clinical and Forensic Science, Clinical Hospital Split, Split, Croatia p Institut f. Rechtsmedizin, Universitaet Mainz, Mainz, Germany q LGC, Lifescience New Ventures Group, Teddington, Middlesex TW11 OLY, UK r Institute of Criminalistics Prague, Prague , Czech Republic Keywords: Forensic genetics; DNA; STR-polymorphisms; PowerPlex Introduction The recently distributed STR typing kit PowerPlexk 16 (Promega, Madison, USA) was evaluated in 17 different European laboratories. The kit amplifies the loci D3S1358, * Corresponding author. Tel.: ; fax: address: bgf.henke@t-online.de (L. Henke) /03 D 2003 Elsevier Science B.V. All rights reserved. PII: S (02)

2 790 L. Henke et al. / International Congress Series 1239 (2003) TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, Amelogenin, vwa, D8S1179, TPOX and FGA. This broad study focused on technical aspects including: the impact of the amount of target DNA, balance of loci, peak height differences in heterozygotes, comparison of genotyping results obtained with different primers as well as the analysis of population data and mutation rates. 2. Methods Each laboratory analysed unrelated individuals from its area with exception of the Teddington laboratory, which investigated individuals from immigration cases which could be assigned to either an Asian group (India, Pakistan and Bangladesh) or African Blacks. DNA was prepared from buccal swabs and blood by various well-established methods partially followed by quantification. PCR reaction volumes other than the recommended 25 Al varied from 10 to 50 Al. The analyses were performed on either an ABI 310 or ABI 377 analyses. Allele designation was performed by comparison with the allelic ladder provided with the kit. The allele frequencies were calculated from the number of each genotype of the sample set. Unbiased estimates of expected heterozygosity were computed as described by Edwards et al [1]. Possible deviation from Hardy Weinberg Equilibrium (HWE) was tested by calculating the unbiased estimate of the expected homozygote/heterozygote frequencies [2 4] and the exact test [5] based on 2000 shuffling experiments. The F ST values were determined as described by Weir and Cockerham [6]. 3. Results and discussion Each laboratory analysed persons which added up to a total number of 3698 individuals. Between 1876 (vwa) and 695 (D16S539), samples were tested with at least one different primer set (loci CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, TPOX and vwa). Results (19,555) were compared. At locus D8S1179, PowerPlexk 16 revealed heterozygotes in two parent/child pairs while amplification with AmpFlSTRR SGM Plus (Applied Biosystems, USA) showed only one allele. The parents were from either Vietnamese or Philippine decent. At locus TH01, one heterozygous sample (6/9.3) (PowerPlexk 16) showed only the allele 9.3 with AmpFlSTRR SGM Plus (ABI). At locus vwa, one person showed the phenotype 16/17 with PowerPlexk 16 while AmpFlSTRR SGM Plus and AmpFlSTRR Profiler 1 (ABI) amplified allele *16 only. Weak amplifications with PowerPlexk 16 were observed at loci FGA ( *24) and TPOX ( *9) in parent /child pairs while balanced peak heights were obtained with AmpFlSTRR Profiler 1 (ABI). At locus D5S818, weak amplifications of allele * 10 were observed with PowerPlexk 16 in two individuals. Locus CSF1PO showed a weak allele *8 with another sample while amplifications with Profiler 1 showed normal peaks. The balance of the amplicons was measured by comparing the mean peak heights from heterozygous loci. The inter loci balance for the blue systems is shown in Fig. 1. The

3 L. Henke et al. / International Congress Series 1239 (2003) Fig. 1. Interloci balance. Mean peak heights (RFU) of heterozygous loci D3 (n = 132), TH01 (n = 128), D21 (n = 134), D18 (n = 133) and Penta E (n = 131). peak height differences (%) in sister alleles of heterozygotes was calculated for the loci D3, TH01, D21, D18 and Penta E with allele 1 as the smaller allele. Most peak height differences were observed in the range from 10% to 30%: D3 (96.6%), TH01 (94.3%), D21 (95.9%), D18 (98.6%) and Penta E (83.5%) (Fig. 2). Peak height differences > 60% can be caused by either technical or genetic reasons. Control amplification with purified DNA can rule out technical reasons while transmission of the weaker allele gives a strong indication of incomplete primer matching in these loci. The allele frequencies of the various European populations were very similar while the Asian group and to a greater extent the group of African Blacks showed considerable differences. The genetic distance between the European populations varies between 0.96 Fig. 2. Peak height differences (%) of the sister alleles in heterozygotes. Allele 1 is the smaller allele.

4 792 Table 1 Allele frequenqies (%) at the locus Penta E, laboratory: Amsterdam (AMS), BERN, Hamburg (HAM), Innsbruck (INN), Koeln (KLN), Ljubljana (LJU), Madrid (MAD), Mainz (MZ), Parma (PAR), Prague (PRA), Rome (ROM), Split (SPL), Genève (SWI), Tallin (TAL), Tuebingen (TUE), Asian Group (TED_A), African Black (TED_B) Number of Alleles individuals tested AMS BERN HAM INN KLN LJU MAD MZ PAR PRA ROM SPL SWI TAL TUE TED_A TED_B L. Henke et al. / International Congress Series 1239 (2003)

5 Table 2 Allele frequenqies (%) at locus Penta D, laboratory: Amsterdam (AMS), BERN, Hamburg (HAM), Innsbruck (INN), Koeln (KLN), Ljubljana (LJU), Madrid (MAD), Mainz (MZ), Parma (PAR), Prague (PRA), Rome (ROM), Split (SPL), Genève (SWI), Tallin (TAL), Tuebingen (TUE), Asian Group (TED_A), African Black (TED_B) Number of Alleles individuals tested AMS BERN HAM INN KLN LJU MAD MZ PAR PRA ROM SPL SWI TAL TUE TED_A TED_B L. Henke et al. / International Congress Series 1239 (2003)

6 794 L. Henke et al. / International Congress Series 1239 (2003) Table 3 Meioses and genetic inconsistencies at loci Penta D and Penta E GEC Maternal meioses Paternal meioses Maternal inconsistencies Paternal inconsistencies Penta D (0.12%) Penta E (0.11%) 1 (0,12%) and Variants were observed at most loci. The frequencies for the loci Penta D and Penta E revealed a high level of polymorphism (Tables 1 and 2). In spite of the high general exclusion rates of Penta D and Penta E, their mutation rates were low (Table 3). All mutations observed at loci other than the Pentas were confirmed by using alternative primer sets. References [1] A. Edwards, H.A. Hammond, L. Jin, C.T. Caskey, R. Chakraborty, Genetic variation at five trimeric and tetrameric repeat loci in four human population groups, Genomics 12 (1992) [2] R. Chakraborty, P.E. Smouse, J.V. Neel, Population amalgation and genetic variation: observation and artificially agglomerated tribal populations of Central and South America, Am. J. Hum. Genet. 43 (1988) [3] M. Nei, Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics 89 (1978) [4] M. Nei, A.K. Roychoudhury, Sampling variances of heterozygosity and genetic distance, Genetics 76 (1974) [5] B. Budowle, B. Shea, S. Niezgoda, R. Chakraborty, CODIS STR loci data from 41 sample populations, J. Forensic Sci. 46 (3) (2001) [6] B.S. Weir, C.C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution 38 (1984)